Re: [Bioc-devel] problem in rbind with DelayedArray / HDF5Array package

Yes that does get around the problem, thanks! I would note, though, that for me at least, its a workaround and not ideal functionality, since to use it in my function means that I now I have to have two different code snippets depending on whether my input object (here `testhdf`) is a matrix

Re: [Bioc-devel] problem in rbind with DelayedArray / HDF5Array package

Does `rbind(testhdf, DelayedArray(testdata))` give you what you want? On Wed, 4 Apr 2018 at 14:58 Elizabeth Purdom wrote: > Hello, > > I am trying to do a rbind a normal (in memory) matrix with a HDF5Matrix > object or DelayedArray object and I am hitting problems.

[Bioc-devel] problem in rbind with DelayedArray / HDF5Array package

Hello, I am trying to do a rbind a normal (in memory) matrix with a HDF5Matrix object or DelayedArray object and I am hitting problems. I’m using the development version of R and bioconductor (as of 2 weeks ago) and HDF5Array_1.7.9, DelayedArray_0.5.23 — see sessionInfo at end of email.

Re: [Bioc-devel] Missed deadline

Kenneth, I agree with Kasper. I generally like the approach of getting the software out there sooner rather than later. Especially if the paper you are talking about is a method paper about the software algorithm, rather than a result paper. In that case, getting it into a public, DOI'ed

[Bioc-devel] web browser support missing in the build system? new package, IGV

Perhaps my newly submitted package times out because no web browser is available on the build systems? https://github.com/paul-shannon/IGV The build times out on linux and OS X at the “creating vignettes” stage. But since the package is a wrapper around igv.js running in the browser, no

Re: [Bioc-devel] Tensorflow support for bioconductor packages

Hi all, Thanks for your replies. I had a look at the greta package (https://github.com/greta-dev/greta) on CRAN that uses tensorflow, which seemingly exports the install_tensorflow function but still requires the user to call it, so it looks like that's the best way to go for now. I'll submit our

[Bioc-devel] Bioc-devel changes and SummarizedExperiment class

Hi Hervé, Some recent changes in bioc-devel are causing trouble with SummarizedExperiment objects if the rowRanges slot inherits from GRangesList. Please see example below. Thanks in advance for your help. Leonard -- > library(SGSeq) > > ## SGVariants object inherits from GRangesList >

[Bioc-devel] BioC 3.7: build failing on Mac (merida2) because Cairo not available

Dear All, A package I maintain (ADaCGH2) is giving an error during build (http://bioconductor.org/checkResults/devel/bioc-LATEST/ADaCGH2/merida2-buildsrc.html) because Cairo is not available. A quick look at other packages that depend on Cairo shows the same problem there. What should we do?

Re: [Bioc-devel] Missed deadline

This is a subjective question. As a paper reviewer I like to see the package accepted. That increases trust. As a package reviewer I like some idea of what the package actually does, so a statement like "we implement X which is described in (XX, in preparation), is also irritating. Unless you're

Re: [Bioc-devel] Missed deadline

Hi Gabe & Levi, Here is my current plan: 1 - complete the requirements checklist ( http://www.bioconductor.org/developers/package-submission/) 2 - get feedback the in-house NGS team, and then from the rest of in-house bioinformatics (others who use R more may spot some issues) 3 - set up pull